_common.R

  # dpi = 300,
  # cache.lazy = FALSE,
  # tidy = "styler",
  # out.width = "90%",
  # fig.align = "center",
  # fig.width = 5,
  # fig.height = 7
  #


### gen.options ###

suppressPackageStartupMessages(library(tidyverse, quietly = T))
library(latex2exp, warn.conflicts = F, quietly = T)
library(patchwork, warn.conflicts = F, quietly = T)
library(knitr, warn.conflicts = F, quietly = T)
options(crayon.enabled = FALSE)



knitr::opts_chunk$set(
  tidy.opts=list(width.cutoff=80),
  tidy=TRUE,
  warning = FALSE,
  collapse = TRUE,
  strip.white = TRUE,
  message = FALSE,
  cache = FALSE,
  echo = FALSE,
  fig.align = "center",
  comment = "#>"
)

## wrapper to plot inla object posteriors quantities

post_plot = function(inla_obj, quantity, coef) {

  if(!inherits(inla_obj, "inla")){
    stop("argument 'inla_obj' should be class 'inla'")

  }

  if(str_detect(coef, "(?i)\\bintercept\\b")) {
    coef = paste0("(",str_to_title(coef),")")
  }

  inla_obj %>%
    pluck(quantity, coef) %>%
    as_tibble() %>%
    ggplot(aes(x, y)) +
    geom_line(aes(x, y)) +
    theme_nicco()

}


theme_nicco = function (base_size = 11, base_family = "") {
  theme_bw() %+replace%
    theme(
      text = element_text(family = "sans", size = 12),
      plot.title = element_text(face = "bold", size = 14, margin=margin(0,0,30,0)),
      panel.background  = element_blank(),
      axis.ticks = element_line(colour = "grey70", size = 0.2),
      plot.background = element_rect(fill="white", colour=NA),
      panel.border = element_rect(linetype = "blank", fill = NA),
      legend.background = element_rect(fill="transparent", colour=NA),
      legend.key = element_rect(fill="transparent", colour=NA)
    )
}


## alt theme
theme_nicco2 = function (base_size = 11, base_family = "") {
  theme_bw() %+replace%
    theme(
      text = element_text(family = "sans", size = 12),
      plot.title = ggplot2::element_text(size = 18, colour = "#454545",hjust = 0.5, margin = ggplot2::margin(b = 10)),
      panel.background  = element_blank(),
      panel.grid.major = ggplot2::element_line(linetype = "dotted",colour = "#454545",size = 0.3),
      panel.grid.minor = ggplot2::element_blank(),
      axis.ticks = element_line(colour = "grey70", size = 0.2),
      axis.line = ggplot2::element_line(color = "#454545", size = 0.3),
      plot.background = element_rect(fill="white", colour=NA),
      panel.border = element_rect(linetype = "blank", fill = NA),
      legend.background = element_rect(fill="transparent", colour=NA),
      legend.key = element_rect(fill="transparent", colour=NA),
      strip.background = ggplot2::element_rect(fill = "transparent",colour = NA),
      axis.title = ggplot2::element_text(size = 13, colour = "#454545",hjust = 0.95),
      axis.text = ggplot2::element_text(size = 10, colour = "#212121"),
      strip.text = ggplot2::element_text(size = 12, colour = "#454545",
                                         margin = ggplot2::margin(10, 10,
                                                                  10, 10,
                                                                  "pt"))
    )
}